Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

Gupta, Radhey S.; Patel, Sudip; Saini, Navneet; Chen, Shu

doi:10.1099/ijsem.0.004475

Cited by 680 publications

(124 citation statements)

References 179 publications

(330 reference statements)

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“…Genome size and base composition are also different. The same situation is found in the METHANOLICUS group, which may also be divided in several groups, as suggested by Gupta et al [16,17]. The SIMPLEX group has a considerable amount of tandem repeats, most of them with a 21 nt repeat, a characteristic feature of this group.…”

Section: Taxonomic Distribution Of Tandem Repeatssupporting

confidence: 68%

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Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Subirana

Messeguer

2021

IJMS

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Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.

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Section: Taxonomic Distribution Of Tandem Repeatssupporting

confidence: 68%

“…In any case, it is clear that further work is required for a complete taxonomic classification, many species do not fit in any group: The genus Bacillus is in need of taxonomic revision [18]. In fact, Gupta et al have recently suggested a division of Bacillus in 25 different groups [16,17].…”

Section: Taxonomic Distribution Of Tandem Repeatsmentioning

confidence: 99%

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Subirana

Messeguer

2021

IJMS

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“…22 Probiotic Weizmannia species (e.g. former Bacillus coagulans) have recently been reclassified, 23 and have an unquestionable probiotic significance. 24 While at least one ARG was found in each metagenomic sample, less than half of the isolates contained any of them.…”

Section: Discussionmentioning

confidence: 99%

Mobile antimicrobial resistance genes in probiotics

Tóth

Csabai

Judge

et al. 2021

Preprint

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Even though people around the world tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they transfer. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

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“…Recently, the genus Bacillus , of 293 species and subspecies, was reclassified on the basis of phylogenomic and comparative genomic frameworks, six genera, Peribacillus , Cytobacillus , Mesobacillus , Neobacillus , Metabacillus and Alkalihalobacillus, were separated from the genus Bacillus [1]. The genus Bacillus has been limited to only the members of the Subtilis and Cereus clade of species [2]. There are 16 species in the genus Peribacillus with validly published names (https://lpsn.dsmz.de/genus/peribacillus), most species of this genus have been isolated from soil [3–10] and plant tissues [11, 12].…”

Section: Full-textmentioning

confidence: 99%

Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow

Jiang

Jung

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-positive, facultatively anaerobic, endospore-forming, rod-shaped strain, AGMB 02131T, which grew at 20–40 °C (optimum 30 °C), pH 3.0–11.0 (optimum pH 4.0) and in the presence of 0–18 % (w/v) NaCl (optimum 10 %), was isolated from a cow faecal sample and identified as a novel strain using a polyphasic taxonomic approach. The phylogenetic analysis based on 16S rRNA gene sequences along with the whole genome (92 core gene sets) revealed that AGMB 02131T formed a group within the genus Peribacillus , and showed the highest sequence similarity with Peribacillus endoradicis DSM 28131T (96.9 %), following by Peribacillus butanolivorans DSM 18926T (96.6 %). The genome of AGMB 02131T comprised 70 contigs, the chromosome length was 4 038 965 bp and it had a 38.5 % DNA G+C content. Digital DNA–DNA hybridization revealed that AGMB 02131T displayed 21.4 % genomic DNA relatedness with the most closely related strain, P. butanolivorans DSM 18926T. AGMB 02131T contains all of the conserved signature indels that are specific for members of the genus Peribacillus . The major cellular fatty acids (>10 %) of AGMB 02131T were C18 : 1ω9c, C18:0 and C16 : 0. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, AGMB 02131T represents a novel species of the genus Peribacillus , for which the name Peribacillus faecalis sp. nov. is proposed. The type strain is AGMB 02131T (=KCTC 43221T=CCTCC AB 2020077T).

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Cited by 680 publications

References 179 publications

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Mobile antimicrobial resistance genes in probiotics

Peribacillus faecalis sp. nov., a moderately halophilic bacterium isolated from the faeces of a cow

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